# Downloading, normalizing and plotting the data
library(pd.hta.2.0)
library(oligo)
celFiles <- list.celfiles()
affyRaw <- read.celfiles(celFiles)
## Reading in : 01-13.3577_(HTA-2_0).CEL
## Reading in : 02-13.3578_(HTA-2_0).CEL
## Reading in : 03-13.3580.2_(HTA-2_0).CEL
## Reading in : 04-13.3582_(HTA-2_0).CEL
## Reading in : 05-13.3623_(HTA-2_0).CEL
## Reading in : 06-13.3627.1_(HTA-2_0).CEL
## Reading in : 07-13.3633_(HTA-2_0).CEL
## Reading in : 08-13.6393.3_(HTA-2_0).CEL
## Reading in : 09-13.6394_(HTA-2_0).CEL
## Reading in : 10-13.12026.2_(HTA-2_0).CEL
## Reading in : 11-13.13283_(HTA-2_0).CEL
## Reading in : 12-16.082_(HTA-2_0).CEL
eset <- rma(affyRaw)
## Background correcting
## Normalizing
## Calculating Expression
boxplot(eset, col=cols)
hist(eset, col=cols)
fit <- fitProbeLevelModel(affyRaw)
NUSE(fit, las = 2, cex.axis = 0.35)
RLE(fit, las = 2, cex.axis = 0.35)
# Annotating the expression set
library(hta20sttranscriptcluster.db)
my_frame <- data.frame(exprs(eset))
x <- hta20sttranscriptclusterSYMBOL
mapped_probes <- mappedkeys(x)
xx <- as.list(x[mapped_probes])
universe <- unlist(xx)
write.table(universe, 'universe.txt', quote =F, sep ='\t',col.names = F, row.names = T)
universe2<-read.table("universe.txt", header = FALSE)
rownames(universe2)<-universe2[,1]
eset_array<-merge(universe2, my_frame, by=0)
dim(eset_array)
## [1] 23964 12
# Plotting raw images and scatter plots
library(affy)
##
## Attaching package: 'affy'
## The following objects are masked from 'package:oligo':
##
## intensity, MAplot, mm, mm<-, mmindex, pm, pm<-, pmindex,
## probeNames, rma
## The following object is masked from 'package:oligoClasses':
##
## list.celfiles
par(mfrow=c(2,6))
image(affyRaw[,1])
image(affyRaw[,2])
image(affyRaw[,3])
image(affyRaw[,4])
